Portland, OR, August 24, 2007 - Schrödinger is pleased to announce the first update release to Schrödinger's 2007 Suite. In addition to general enhancements to existing products, this update release also marks the beta release of Schrödinger's KNIME Extensions.

Click here for a PDF of the Product Feature list for the update release of Schrödinger Suite 2007. To download the update release, please visit the Download Center .

 New Product

KNIME Extensions 1.0.032

KNIME (www.knime.org) is an open source pipelining program that provides a graphical interface for building workflows. Most of Schrödinger's tools have been integrated as KNIME Extensions, providing components within KNIME for building workflows.

Updates to Existing Products

CombiGlide/Core Hopping 1.5.107 [Visit Product page]

• Better support for use of Epik for reagent preparation - fixed bug that caused elimination of reagents containing a nitrogen atom as the first non-leaving atom
• Ability to define constraints from the Core Hopping Protocore Docking panel
• Core-Hopping Visualization panel provides a convenient way to view results
• Raw Core Editing Panel provides a way to specify custom attachment points interactively for use in protocore alignment
• Using the ‘R#' atom type on terminal atoms in an SD file will specify only such atoms as allowed attachment points for protocore preparation, thus allowing automated preparation of protocores with specified attachment points from molecules downloaded from a database

Epik 1.5.207 [Visit Product page]

[none]

Glide 4.5.208 [Visit Product page]

• Expanded Glide workflow to utilize structures in compressed Maestro format
• Fixed a bug in finding grid files specified with relative paths when running remotely
• Fixed a bug in XP Glide where some calculations would fail to run to completion
• Fixed a memory leak in XP Refinement jobs
• Improved behavior when a ligand outside a binding site is provided as input for a Refinement experiment
• Fixed a bug where an HTVS experiment with post-docking minimization and constraints could lead job failure
• Fixed a bug where RMSDs were being incorrectly computed
• Fixed a bug where legacy licenses would in some cases not be recognized

Jaguar 7.0.207 [Visit Product page]

• Added 4 new density functionals from the Truhlar group: M06, M06-2X, M06-L, M06-HF
• Fixed bug in the M05-2X correlation functional that caused calculated energies to be incorrect
• Fixed bug that prevented Jaguar batch scripts like hydrogen_bond.py from being used with queues
• Fixed bug that prevented solvation jobs from being run in parallel (MPI) on the ia64 architecture
• Added more modes of operation to the hydrogen_bond.py script for calculating binding energies of hydrogen-bonded complexes

Liaison 4.5.208 [Visit Product page]

[none]

LigPrep 2.1.207 [Visit Product page]

• Fixed bug in which cage-like molecules (e.g., adamantine) would sometimes not produce the correct number of output structures

MacroModel 9.5.207 [Visit Product page]

• New graphical interface for angle/distance driver (Applications>MacroModel>Coordinate Scan)

Maestro 8.0.308 [Visit Product page]

• Python scripts can be updated directly from the Schrödinger website
• Spacebar can now be used reliably to temporarily enter into global or local transformation mode
• Fixed several bugs that caused Maestro to crash

MCPRO+ 2.0.208

• New "Examine SAR" interface to predict relative binding affinities and understand structure-activity relationships - from a protein-ligand complex, specification of the ligand R-group to be examined and selection of substitution fragments would automatically set up and execute experiments to calculate relative binding affinities, via FEP, between ligands and the selected substitution fragments
• Revised Linear Response user interface for greater consistency with other MCPRO+ workflows
• For FEP, DDG, and LRM runs improved near real-time monitoring of configuration geometry
• New checkpoint files enable simple simulation restarting
• Fixed bug where output geometries in Monte Carlo sampling would sometimes be physically unreasonable but exhibit reasonable energies
• Fixed bug where minimized geometries from preminimization in FEP, DDG, or LRM runs would see an incorrect vdW potential
• Fixed bug in finding structural output for Maestro incorporation

Phase 2.5.207 [Visit Product page]

• Fixed bug in MacroModel's Ligand Torsion Sampling algorithm that caused Phase conformational search to fail on molecules containing aromatic rings bonded to adjacent atoms on an aromatic ring
• Improved performance of adding molecules to a database via phasedb_manage
• Fixed inconsistencies in phasdb_confsites and phasedb_subset regarding which molecules lack conformers
• Fixed bug in phase_dbsearch that prevented restarting of subjobs which did not complete at least one block
• Fixed bug in phase_gridSearch that prevented automatic rerunning of portions of the calculation that fail because of license errors
• Improved partial matching performance in all searching backends
• Find Matches to Hypothesis now supports remote database searching

Prime 1.6.307 [Visit Product page]

• Implicit membrane model with a graphical interface for setting up the membrane region
• Fixed bug that prevented Prime from being run on multi-chain proteins containing capping groups
• Fixed bug that prevented editing of the secondary structure prediction in the Prime Sequence Viewer
• Fixed bug that prevented selection across rows in the Prime Sequence Viewer

PrimeX 1.0.307 [Visit Product page]

• Support for map generation and real-space refinement using imported phased reflections
• Significant speed up of crystal mate generation
• Support for reading and writing CCP4 format electron density maps
• Output PDB files have an informative header reflecting results of each step
• Covalently-bonded arsenic compounds (e.g., cacodylate) are now supported
• Test set flag of 0 or 1 supported for imported mtz files
• Intensity data in PDB mmCIF files converted to amplitudes by ‘refconvert' utility

QikProp 3.0.207 [Visit Product page]

• Fixed bug that caused QikProp to halt when encountering ligands with Boron or other unsupported atoms
• Fixed bug where job names were sometimes derived from the input file rather than using a user-requested jobname

QSite 4.5.208 [Visit Product page]

• Fixed bug which prevented backbone cuts in HIS from being accepted when the force field was OPLS_2005

SiteMap 2.1.208 [Visit Product page]

[none]

Strike 1.6.308 [Visit Product page]

[none]

XP Visualizer 4.5.208

• Fixed bug in which ligands without titles were not properly displayed

Updates to Existing Solutions/Workflows

Induced Fit Docking (IFD) [Visit Solution page]

• Support for metal constraints
• Fixed bug that affected use of user-supplied Glide Pose Viewer (pv) file
• Additional support for Prime specific functions through addition of keywords directly in the IFD input file (e.g., USE_MAE_CHARGES)

Job Control and Licensing

[none]

QM-Polarized Ligand Docking [Visit Solution page]

[none]

Protein Preparation Wizard [Visit Solution page]

• Several improvements to usability and robustness

Virtual Screening Workflow (VSW)

• Support for H-bond and metal constraints
• Improved robustness

• GPCR helix manipulator
• Interface for ligand property filtering
• Interaction energies between receptor residues and ligand groups
• Binding site alignment of multiple proteins